Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate 3606642 Dshi_0074 acetyl-CoA acetyltransferase (RefSeq)
Query= uniprot:D8ITH5 (401 letters) >FitnessBrowser__Dino:3606642 Length = 392 Score = 254 bits (648), Expect = 4e-72 Identities = 159/398 (39%), Positives = 230/398 (57%), Gaps = 15/398 (3%) Query: 5 ICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAGEDNR 64 IC A RTP G + G V A L A I + + GV ++V ++L GC AG+ + Sbjct: 6 ICGAARTPMGGFQGVFSDVSAAQLGGAAIAGALA-DAGVAPAQVNELLMGCVLPAGQ-GQ 63 Query: 65 NVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMTRAPF 124 AR AG AGL AVP +T+N++CGS + A +A I G+ L++AGG+ESMT AP+ Sbjct: 64 APARQAGYAAGLGDAVPATTLNKMCGSGMKAAMIACDQIALGQSDLVVAGGMESMTNAPY 123 Query: 125 VMGKAESAFARSAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQDAFA 184 ++ K AR I F++ L A M AE+ A FQ RA QD +A Sbjct: 124 LLDKMRGG-ARIG--HGQVIDHMFLDGLEDAYDKGRLMGTFAEDCAEAFQFTRAAQDTYA 180 Query: 185 LRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHP---RPDTTLATLAKLKGVV 241 L S + AA+A+ FA E+ P+T+ +KG+ +V+ DE P RP+ + LK Sbjct: 181 LGSLENALAAEASEAFAMELVPVTVSGRKGETVVIR-DEQPAAARPEK----IPHLKPAF 235 Query: 242 RPDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAPA 301 R DGTVTA N+S ++DGA AL+LA A+ + L RARVLG A+ P + P PA Sbjct: 236 RKDGTVTAANSSSISDGAAALVLADAGQAEAHGLPVRARVLGHASHAQKPALFPTAPVPA 295 Query: 302 VRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGAS 361 RK+L ++G +A +D+ E+NEAFA +A M ++G+P + +N NGGA A+GHP+GAS Sbjct: 296 ARKLLDRLGWCVADVDLWEVNEAFAVVPMAFMHEMGVPRE--KMNVNGGACALGHPIGAS 353 Query: 362 GARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIER 399 GAR++ T +N +E + + +CIG G+G A+ +ER Sbjct: 354 GARILVTLLNAMEARDLKRGVAAICIGGGEGTAIALER 391 Lambda K H 0.320 0.135 0.394 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 402 Number of extensions: 19 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 401 Length of database: 392 Length adjustment: 31 Effective length of query: 370 Effective length of database: 361 Effective search space: 133570 Effective search space used: 133570 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory